A target enrichment probe set for resolving the flagellate land plant tree of life

Abstract

Premise: New sequencing technologies facilitate the generation of large-scale molecular data sets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms.

Methods: We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages.

Results: Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics.

Conclusions: A target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate land plants.

Keywords: flagellate plants; next‐generation sequencing; nuclear loci; phylogenomics; target enrichment.

FIGURE 1

Distribution of the number of successfully sequenced loci (out of a possible 451) per taxon sample. Each locus is a relatively conserved exon from a single‐copy or low‐copy nuclear gene.

FIGURE 2

Associations of the amount of DNA and number of reads with the number of resulting loci from a sample. (A) Amount of library DNA in each sample vs. the number of resulting loci obtained in the targeted enrichment analysis. The dashed line at 250 ng represents the amount of DNA at which samples were normalized for the library preparation. (B) Number of reads obtained from each sample vs. the number of loci obtained from the targeted enrichment analysis.

FIGURE 3

Heat map showing the distribution of data in the flagellate plant samples across the 451 probe regions (i.e., exons). Loci that were missing for an individual are colored blue in the heatmap while sampled loci are grey. Black bars along the bottom of the heatmap indicate loci with biases among major plant groups, where less than 25% of one group had the locus and over 75% of another group had the locus.

FIGURE 4

Phylogram from a maximum likelihood analysis of the supermatrix made by concatenating the alignments from the GoFlag 451 probe regions (i.e., exons) for the samples with at least 45 loci. The tree was rooted between the bryophytes and vascular plants.